data_3BG5 # _model_server_result.job_id OC9TxbcVx60qzxqJgaePcQ _model_server_result.datetime_utc '2024-11-13 17:36:55' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3bg5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":2001}' # _entry.id 3BG5 # _exptl.entry_id 3BG5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.062 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYRUVIC ACID' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.47 _cell.angle_gamma 90 _cell.entry_id 3BG5 _cell.length_a 96.428 _cell.length_b 256.083 _cell.length_c 126.01 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BG5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 1 1 A,C,E,F,G,H,L,M,N,O 2 1 B,D,I,J,K,P,Q,R 3 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 K N N ? 4 N N N ? 4 R N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C SER 305 A SER 315 1_555 A N GLY 306 A GLY 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C PRO 505 A PRO 513 1_555 A N ASN 506 A ASN 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C VAL 757 A VAL 763 1_555 A N ASP 758 A ASP 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C GLU 842 A GLU 849 1_555 A N SER 843 A SER 852 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale5 A NZ LYS 1135 A LYS 1144 1_555 F C11 BTI . A BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 B C SER 305 B SER 315 1_555 B N GLY 306 B GLY 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale7 B C PRO 505 B PRO 513 1_555 B N ASN 506 B ASN 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 B C VAL 757 B VAL 763 1_555 B N ASP 758 B ASP 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale9 B C GLU 842 B GLU 849 1_555 B N SER 843 B SER 852 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 B NZ LYS 1135 B LYS 1144 1_555 J C11 BTI . B BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale11 C C SER 305 C SER 315 1_555 C N GLY 306 C GLY 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale12 C C PRO 505 C PRO 513 1_555 C N ASN 506 C ASN 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale13 C C VAL 757 C VAL 763 1_555 C N ASP 758 C ASP 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale14 C C GLU 842 C GLU 849 1_555 C N SER 843 C SER 852 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale15 C NZ LYS 1135 C LYS 1144 1_555 M C11 BTI . C BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale16 D C SER 305 D SER 315 1_555 D N GLY 306 D GLY 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale17 D C PRO 505 D PRO 513 1_555 D N ASN 506 D ASN 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale18 D C VAL 757 D VAL 763 1_555 D N ASP 758 D ASP 765 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale19 D C GLU 842 D GLU 849 1_555 D N SER 843 D SER 852 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale20 D NZ LYS 1135 D LYS 1144 1_555 Q C11 BTI . D BTI 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 B OD1 ASP 565 B ASP 572 1_555 I MN MN . B MN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc2 D OD1 ASP 565 D ASP 572 1_555 P MN MN . D MN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? # _chem_comp.formula 'C3 H4 O3' _chem_comp.formula_weight 88.062 _chem_comp.id PYR _chem_comp.mon_nstd_flag . _chem_comp.name 'PYRUVIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C O PYR doub 356 n n C OXT PYR sing 357 n n C CA PYR sing 358 n n OXT HXT PYR sing 359 n n CA O3 PYR doub 360 n n CA CB PYR sing 361 n n CB HB1 PYR sing 362 n n CB HB2 PYR sing 363 n n CB HB3 PYR sing 364 n n # _atom_sites.entry_id 3BG5 _atom_sites.fract_transf_matrix[1][1] 0.01037 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003666 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003905 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008417 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 MN A 1 2002 2002 MN MN . F 3 BTI A 1 2000 2000 BTI BTI . G 4 PYR A 1 2001 2001 PYR PYR . H 5 ATP A 1 2100 2100 ATP ATP . I 2 MN B 1 2002 2002 MN MN . J 3 BTI B 1 2000 2000 BTI BTI . K 4 PYR B 1 2001 2001 PYR PYR . L 2 MN C 1 2002 2002 MN MN . M 3 BTI C 1 2000 2000 BTI BTI . N 4 PYR C 1 2001 2001 PYR PYR . O 5 ATP C 1 2100 2100 ATP ATP . P 2 MN D 1 2002 2002 MN MN . Q 3 BTI D 1 2000 2000 BTI BTI . R 4 PYR D 1 2001 2001 PYR PYR . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C PYR . . . G 4 85.234 119.46 -21.312 1 93.6 ? C PYR 2001 A 1 HETATM 2 O O PYR . . . G 4 86.359 119.783 -21.91 1 93.64 ? O PYR 2001 A 1 HETATM 3 O OXT PYR . . . G 4 85.185 118.392 -20.549 1 93.5 ? OXT PYR 2001 A 1 HETATM 4 C CA PYR . . . G 4 84.101 120.251 -21.494 1 93.59 ? CA PYR 2001 A 1 HETATM 5 O O3 PYR . . . G 4 83.089 119.79 -22.192 1 93.18 ? O3 PYR 2001 A 1 HETATM 6 C CB PYR . . . G 4 84.042 121.631 -20.9 1 93.72 ? CB PYR 2001 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 123 _model_server_stats.query_time_ms 369 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 6 #